The invention provides a hydrogeneration system of hydrogen compressor skid-mounted hydrogeneration equipment and a hydrogenation method. The system comprises the following components arranged insidea skid-mounted shell: a pressurizing component, a hydrogen dispenser, a circulation loop and a controller, wherein a gas inlet of a diaphragm compressor in the pressurizing component is connected witha hydrogen inlet pipe, the end of the hydrogen inlet pipe is provided with an input end connected with a gas outlet of a hydrogen transporting truck, a gas outlet of the diaphragm compressor is connected with a hydrogen outlet pipe, and hydrogen in the hydrogen outlet pipe is cooled when flowing through a first cooling heat exchange element; a gas inlet pipeline of the hydrogen dispenser is connected with the hydrogen outlet pipe, and hydrogen in the gas inlet pipeline is cooled when flowing through a second cooling heat exchange element; one end of the circulation loop communicates with thehydrogen inlet pipe, and the other end of the circulation loop communicates with the hydrogen outlet pipe; and a first control valve, a second control valve and a third control valve which are used for controlling on and off of the pipelines are arranged on the hydrogen inlet pipe, the hydrogen outlet pipe and the circulation loop correspondingly, and are all connected with the controller. The whole hydrogeneration system is compact in structural arrangement, small in occupied area, and large in hydrogeneration capacity.